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@BioImageTools

BioImageTools

README.md

BioImageTools

Shared GitHub organization for work related to OME-Zarr and scalable bioimage analysis workflows.

This org was created at the 2023 Next generation bioimage analysis workflows hackathon held at the BioVisionCenter at UZH, for the purposes of continuing collaboration and innovation on NGFF-based and FAIR image processing workflows. Continued at the 2024 OME-NGFF workflows hackathon

We are interested in...

  • Bioimage tools which consume and/or produce OME-Zarr
  • OCI containers
  • Nextflow modules and subworkflows
  • Galaxy integrations
  • Fractal integrations
  • OME-Zarr usage examples
  • OME-Zarr performance evaluation
  • OME-Zarr 0.5 tool evaluation
  • ...

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  1. containers containers Public

    Python 3 2

  2. nextflow-modules nextflow-modules Public

    nf-core-compatible modules for Nextflow

    Nextflow 2 1

Repositories

Showing 10 of 13 repositories
  • iss-nf Public

    Reusable in-situ sequencing analysis workflow orchestrated by Nextflow

    BioImageTools/iss-nf’s past year of commit activity
    Python 1 MIT 0 2 0 Updated Mar 17, 2025
  • .github Public
    BioImageTools/.github’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Mar 13, 2025
  • ome-zarr-fiji-java Public

    A drag-and-drop gateway of OME-Zarrs into Fiji.

    BioImageTools/ome-zarr-fiji-java’s past year of commit activity
    Java 0 BSD-2-Clause 0 0 0 Updated Jan 16, 2025
  • ngff-transformations Public
    BioImageTools/ngff-transformations’s past year of commit activity
    Python 4 MIT 0 1 0 Updated Nov 23, 2024
  • zarr-chunk-benchmarking Public

    2024 OME-Zarr Hackathon project for benchmarking read performance of chunk sizing on different storage environments

    BioImageTools/zarr-chunk-benchmarking’s past year of commit activity
    Python 2 0 0 0 Updated Nov 22, 2024
  • single-file-ome-ngff Public
    BioImageTools/single-file-ome-ngff’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Nov 21, 2024
  • ome-zarr-parallel-write Public

    ome-zarr-parallel-write outcome @ OME-NGFF workflow hackathon

    BioImageTools/ome-zarr-parallel-write’s past year of commit activity
    0 0 0 0 Updated Nov 19, 2024
  • ome-zarr-image-analysis-nextflow Public

    Basic example of using OME-Zarr in a Nextflow pipeline

    BioImageTools/ome-zarr-image-analysis-nextflow’s past year of commit activity
    Jupyter Notebook 16 MIT 2 7 0 Updated Nov 16, 2024
  • containers Public
    BioImageTools/containers’s past year of commit activity
    Python 3 BSD-3-Clause 2 1 0 Updated Sep 26, 2024
  • test-datasets Public
    BioImageTools/test-datasets’s past year of commit activity
    1 BSD-3-Clause 0 0 0 Updated Apr 2, 2024
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